CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		TurboFold(seed)
MCC	0.611	>	0.560
Average MCC ± 95% Confidence Intervals	0.637 ± 0.230	>	0.565 ± 0.318
Sensitivity	0.593	>	0.533
Positive Predictive Value	0.640	>	0.602
Total TP	89	>	80
Total TN	9709	<	9715
Total FP	64	<	66
Total FP CONTRA	22	>	17
Total FP INCONS	28	<	36
Total FP COMP	14	>	13
Total FN	61	<	70
P-value	0.0

Comparison of performance of Contrafold and TurboFold(seed). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for Contrafold and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and TurboFold(seed). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for Contrafold and TurboFold(seed)).

Total Scores
MCC	0.611
Average MCC ± 95% Confidence Intervals	0.637 ± 0.230
Sensitivity	0.593
Positive Predictive Value	0.640
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.565 ± 0.318
Sensitivity	0.533
Positive Predictive Value	0.602
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.